A Parallel Monte Carlo Code for Simulating Collisional N-body Systems

We present a new parallel code for computing the dynamical evolution of collisional N-body systems with up to N~10^7 particles. Our code is based on the the Henon Monte Carlo method for solving the Fokker-Planck equation, and makes assumptions of spherical symmetry and dynamical equilibrium. The principal algorithmic developments involve optimizing data structures, and the introduction of a parallel random number generation scheme, as well as a parallel sorting algorithm, required to find nearest neighbors for interactions and to compute the gravitational potential. The new algorithms we introduce along with our choice of decomposition scheme minimize communication costs and ensure optimal distribution of data and workload among the processing units. The implementation uses the Message Passing Interface (MPI) library for communication, which makes it portable to many different supercomputing architectures. We validate the code by calculating the evolution of clusters with initial Plummer distribution functions up to core collapse with the number of stars, N, spanning three orders of magnitude, from 10^5 to 10^7. We find that our results are in good agreement with self-similar core-collapse solutions, and the core collapse times generally agree with expectations from the literature. Also, we observe good total energy conservation, within less than 0.04% throughout all simulations. We analyze the performance of the code, and demonstrate near-linear scaling of the runtime with the number of processors up to 64 processors for N=10^5, 128 for N=10^6 and 256 for N=10^7. The runtime reaches a saturation with the addition of more processors beyond these limits which is a characteristic of the parallel sorting algorithm. The resulting maximum speedups we achieve are approximately 60x, 100x, and 220x, respectively.Comment: 53 pages, 13 figures, accepted for publication in ApJ Supplement

Observations on Factors Affecting Performance of MapReduce based Apriori on Hadoop Cluster

Designing fast and scalable algorithm for mining frequent itemsets is always being a most eminent and promising problem of data mining. Apriori is one of the most broadly used and popular algorithm of frequent itemset mining. Designing efficient algorithms on MapReduce framework to process and analyze big datasets is contemporary research nowadays. In this paper, we have focused on the performance of MapReduce based Apriori on homogeneous as well as on heterogeneous Hadoop cluster. We have investigated a number of factors that significantly affects the execution time of MapReduce based Apriori running on homogeneous and heterogeneous Hadoop Cluster. Factors are specific to both algorithmic and non-algorithmic improvements. Considered factors specific to algorithmic improvements are filtered transactions and data structures. Experimental results show that how an appropriate data structure and filtered transactions technique drastically reduce the execution time. The non-algorithmic factors include speculative execution, nodes with poor performance, data locality & distribution of data blocks, and parallelism control with input split size. We have applied strategies against these factors and fine tuned the relevant parameters in our particular application. Experimental results show that if cluster specific parameters are taken care of then there is a significant reduction in execution time. Also we have discussed the issues regarding MapReduce implementation of Apriori which may significantly influence the performance.Comment: 8 pages, 8 figures, International Conference on Computing, Communication and Automation (ICCCA2016

86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy

We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that the GPU version is 7 times faster than the CPU version with the same power consumption. The code can scale up to the entire Summit supercomputer. For a copper system of 113, 246, 208 atoms, the code can perform one nanosecond MD simulation per day, reaching a peak performance of 86 PFLOPS (43% of the peak). Such unprecedented ability to perform MD simulation with ab initio accuracy opens up the possibility of studying many important issues in materials and molecules, such as heterogeneous catalysis, electrochemical cells, irradiation damage, crack propagation, and biochemical reactions.Comment: 29 pages, 11 figure